The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
Ontology for Biomarkers of Clinical Interest
The Ontology for Biomarkers of Clinical Interest is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/obci for details.
Use the Hermit reasoner in Protege to see the correct hierarchy.
A relationship between a biomarker 'c' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'c' provides clinical information about 'd'.
This does not imply that 'c' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'e' that stands in a direct causal relationship with 'c' and 'd'.
A relationship between a biomarker 'c' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'c' is used to infer the presence or occurrence of 'd' or determine its subtype.
A relationship between a serially-measured biomarker 'c' and a disease or condition of clinical interest 'd' or exposure agent 'e', where 'c' is used to infer the status of 'd' or provide evidence of exposure to (or effect of) 'e'.
A relationship between a biomarker 'c' and an exposure agent 'e', where 'c' is used to show that a biological response to 'e' has occurred.
A relationship between a biomarker 'c' and an exposure agent 'e', where 'c' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'.
A relationship between a biomarker 'c' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'c' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'.
A relationship between a biomarker 'c' and an exposure agent 'e', where 'c' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'.
'Level' here can refer to raw counts, percentages, ratios, concentrations, activities, etc.
A relationship between a biomarker 'c' and an exposure agent 'd', where the effect of exposure to 'd' is correlated with the presence or occurrence of 'c', and the observation of 'c' is used to infer exposure to 'd'.
A relationship between a biomarker 'c' and its purpose as defined by the BEST classification system.
A relationship between a biomarker 'c' and its evidence type as defined by the CIViC classification system.
'Level' here can refer to raw counts, percentages, ratios, concentrations, etc.
A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions.
We make a distinction between 'biomarker' and 'biomarker assessed entity'. The former derives from result of measurement or observation of the latter. For example, in and of itself, 'blood sugar' is not considered a biomarker in our treatment, but 'elevated blood sugar' is. Another example is BRCA1; despite appearing on lists of cancer-implicated genes, BRCA1 is _not_ a biomarker of cancer in our treatment. However, the presence of a particular allele of BRCA1 can be a biomarker, or BRCA1 over-expression can be a biomarker.
Biomarkers require comparison between characteristics of interest obtained in test cases vs those in normal cases. What is considered 'normal' will depend on the biomarker; in some cases the comparison will be to a population average, in others it will be to an individual's known healthy state.
Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. A biomarker is not an assessment of how an individual feels, functions, or survives.
A biomarker that is used to detect or confirm the presence of a disease or condition of interest or to identify individuals with a subtype of the disease.
For a perfect diagnostic biomarker test, all patients with the disease or disease subset would be detected (100% sensitivity, i.e., the fraction of people with disease who test positive) and no patients without the disease would be diagnosed with the disease (100% specificity, i.e., the fraction of people without the disease who test negative). In practice no biomarker test has perfect clinical and analytical sensitivity and specificity. [NCBI:books/NBK402285]
Per CIVic, such biomarkers can help a clinician diagnose or exclude a particular disease.
A biomarker that is measured serially to assess the status of a disease or medical condition, or for evidence of exposure to (or effect of) a medical product or an environmental agent.
A biomarker that is used to show that a biological response has occurred in an individual who has been exposed to a medical product or an environmental agent.
A biomarker that is used to identify individuals who are more likely than similar individuals without the biomarker to experience a favorable or unfavorable effect from exposure to a medical product or an environmental agent.
Per CIVic, such biomarkers help predict drug sensitivity or therapeutic response and are valuable in deciding further treatments. Predictive evidence items often explain mechanisms of drug resistance.
A biomarker that is used to identify the likelihood of a clinical event, disease recurrence or progression in patients who have the disease or medical condition of interest.
Per CIVic, such biomarkers are those that predict survival outcome.
A biomarker that is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect. Such biomarkers are measured before and after exposure to a medical product or an environmental agent.
A biomarker that is used to indicate the potential for developing a disease or medical condition in an individual who does not currently have clinically apparent disease or the medical condition.
Per CIVic, such biomarkers are those that indicate an increased likelihood of developing a particular disease.
A biomarker that provides clinical information about a disease.
A biomarker that provides clinical information about COVID-19.
A biomarker that provides clinical information about cancer.
A biomarker that indicates the clinical effect of or response to exposure to a substance.
A biomarker that is assessed using urine as the anatomical source.
A biomarker that is assessed using blood plasma as the anatomical source.
A biomarker that provides clinical information about some current or potential medical condition.
A biomarker that has an indicated BEST category.
A biomarker that has an indicated assessed entity.
biomarker with specified assessed entity
A biomarker that has an indicated clinical focus.
A biomarker that has an indicated anatomical source.
biomarker with specified anatomical source
A biomarker in which the assessed entity is a physiological characteristic.
This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
A biomarker in which the assessed entity is a cell.
A biomarker in which the assessed entity is a genetic variation.
Genetic variation can be assessed via direct sequencing of genetic material or can be inferred from protein (for example, by using sequence-specific antibodies).
A biomarker in which the assessed entity is a glycan.
A biomarker in which the assessed entity is a small molecule.
A biomarker in which the assessed entity is an RNA.
A biomarker that is assessed using exhaled breath as the anatomical source.
A biomarker that is indicated by an above normal level of propanol determined using a sample of exhaled breath.
A biomarker that is indicated by an above normal level of ethyl butanoate determined using a sample of exhaled breath.
ethyl butanoate in exhaled breath above normal
A biomarker that is assessed using blood as the anatomical source.
A biomarker that is indicated by a below normal level of potassium determined using a sample of blood plasma.
A biomarker that is indicated by a below normal level of sodium determined using a sample of blood.
A biomarker in which the assessed entity is a protein-containing molecular entity.
A biomarker that is indicated by an above normal fibrinogen-to-albumin ratio determined using a sample of blood.
fibrinogen-to-albumin ratio in blood above normal
A biomarker in which the assessed entity is a molecular entity.
A biomarker that is measured serially to assess the status of a disease or medical condition.
monitoring biomarker - clinical condition
A biomarker that is measured serially to assess exposure to (or effect of) a medical product or an environmental agent.
monitoring biomarker - exposure
A biomarker that is indicated by the presence of polymorphism rs567534295 in the BRCA1 gene.
presence of BRCA1 polymorphism rs567534295
A biomarker that is indicated by the presence of polymorphism rs12674822 in the ANGPT2 gene.
presence of ANGPT2 polymorphism rs12674822
A biomarker that is assessed using cerebrospinal fluid as the anatomical source.
A biomarker that is indicated by a below normal level of potassium determined using a sample of urine.
A biomarker that provides clinical information about some respiratory system disease.
A biomarker that provides clinical information about some cognitive disorder.
A biomarker that provides clinical information about some disease by infectious agent.
biomarker of disease by infectious agent
A biomarker that provides clinical information about some disease of anatomical entity.
biomarker of disease of anatomical entity
A biomarker that provides clinical information about some cardiovascular system disease.
biomarker of cardiovascular system disease
A biomarker that provides clinical information about some endocrine system disease.
A biomarker that provides clinical information about some gastrointestinal system disease.
biomarker of gastrointestinal system disease
A biomarker that provides clinical information about some hematopoietic system disease.
biomarker of hematopoietic system disease
A biomarker that provides clinical information about some immune system disease.
A biomarker that provides clinical information about some integumentary system disease.
biomarker of integumentary system disease
A biomarker that provides clinical information about some musculoskeletal system disease.
biomarker of musculoskeletal system disease
A biomarker that provides clinical information about some nervous system disease.
A biomarker that provides clinical information about some reproductive system disease.
biomarker of reproductive system disease
A biomarker that provides clinical information about some thoracic disease.
A biomarker that provides clinical information about some urinary system disease.
A biomarker that provides clinical information about some disease of cellular proliferation.
biomarker of disease of cellular proliferation
A biomarker that provides clinical information about some disease of metabolism.
A biomarker that provides clinical information about some genetic disease.
A biomarker that is assessed using saliva as the anatomical source.
A biomarker that is indicated by an above normal neutrophil-to-lymphocyte ratio determined using a sample of blood.
neutrophil-to-lymphocyte ratio in blood above normal
A biomarker that is indicated by an above normal level of neuron-specific enolase determined using a sample of blood.
neuron-specific enolase in blood above normal
A biomarker that is indicated by an above normal level of soluble urokinase plasminogen activator receptor determined using a sample of blood.
soluble urokinase plasminogen activator receptor in blood above normal
A biomarker in which the assessed entity is some DNA.
This class includes cases where the assessed entity is whole DNA; that is, without regard to sequence.
A defined characteristic or set of characteristics derived from two or more data sources evaluated through an algorithm as an indicator of normal biological processes, pathogenic processes or responses to an exposure or intervention, including therapeutic interventions and environmental exposures.
A biomarker that is assessed using blood serum as the anatomical source.
A biomarker in which the assessed entity is a vocal characteristic.
A biomarker in which the assessed entity is blood pressure.
A biomarker that is indicated by a below normal level of microRNA-214 determined using a sample of urine.
A biomarker that is indicated by an above normal level of beta-hexosaminidase determined using a sample of blood.
beta-hexosaminidase level in blood above normal
A biomarker in which the assessed entity is some bodily movement.
A biomarker in which the assessed entity is some manner of walking.
A biomarker in which the assessed entity is an ocular characteristic.
A biomarker that is indicated by an above normal level of eye redness.
A biomarker that is indicated by an above normal level of sclera irritation.
A biomarker in which the assessed entity is cellular morphology.
A biomarker that is indicated by the presence of ethanol determined using a sample of blood.
A ratio between the level of neutrophils and the level of lymphocytes.
A ratio between the level of fibrinogen and the level of albumin.